An in-gel digestion method of chymotrypsin to improve sequence coverage of membrane protein by mass spectrometry / 生物工程学报

In recent years, mass spectrometry has been widely used to study membrane protein structure and function. However, the application of mass spectrometry to study integral membrane protein is limited because there are many hydrophobic amino acids in the trans-membrane domain of integral membrane protein to cause low sequence coverage detected by LC-MS/MS. Therefore, we used vitamin K epoxide reductase (VKORC1), a human integral membrane protein, as a model to optimize the digestion conditions of chymotrypsin, and developed an in-gel digestion method of chymotrypsin to improve sequence coverage of membrane protein by mass spectrometry. By exploring the effects of calcium concentration, pH value and buffer system on the percentage of sequence coverage, number of total detected and types of unique peptide, and the size of unique peptide, sequence coverage and peptide diversity could be considered under condition of Tris-HCl buffer with 5-10 mmol/L calcium ion concentration and pH value 8.0-8.5. This method could make the sequence coverage of membrane protein to reach more than 80%. It could be widely used in the study of membrane protein structure and function, identification of interaction site between membrane proteins, and identification of binding site between membrane protein and small molecular drug.

Is there any association between osteoporotic vertebral fracture and vitamin K epoxide reductase complex subunit-1 polymorphism in Turkish society? A pilot study

OBJECTIVE: In this study, the relationship between osteoporotic vertebral fractures and 9041 Guanine/Adenine and 3673 Guanine/Adenine polymorphisms related to the vitamin K epoxide reductase complex subunit-1 (VKORC1) gene in postmenopausal women with osteoporosis was investigated. METHOD: DNA was isolated from blood samples collected from 150 women with postmenopausal osteoporosis. Genotyping of the two polymorphic regions (9041 Guanine/Adenine and 3673 Guanine/Adenine) in VKORC1 was performed using polymerase chain reaction-restriction fragment length polymorphism analysis. The presence of radiographic fractures among the 150 patients was ascertained by using the Genant method. RESULT: At least one fracture was detected in 98 patients, and no fracture was observed in 52 patients on radiological images. We found no association between the 9041 Guanine/Adenine (p=0.283) and 3673 Guanine/Adenine (p=0.232) polymorphisms of the VKORC1 gene and the development of secondary postosteoporotic fractures in our study. CONCLUSION: There was no relationship between osteoporotic vertebral fracture and VKORC1 gene polymorphism in a postmenopausal Turkish population.

Study on fluorescence PCR-melting curve method for detecting CYP2C9 and VKORC1 gene polymorphism in Xinjiang Hui population / 国际检验医学杂志

Objective To use the fluorescence PCR‐melting curve method to detect CYP2C9 and VKORC1 gene polymorphism in Xinjiang Hui population ,to analyze their gene distribution and gene mutation frequency ,and to evaluate the clinical applicability of the fluorescence PCR‐melting curve method .Methods The fluorescence PCR‐melting curve method and sequencing method were adopted to contrastively detect CYP2C9*2 ,CYP2C9*3 and VKORC1(‐1639G/A)gene polymorphism .Results Among detected 228 Xinjiang Hui individuals ,199 cases of CYP2C9*1/*1 ,2 cases of CYP2C9*1/*2 ,26 cases of CYP2C9*1/*3 and only 1 case of CYP2C9*3/*3 were detected ,no case of CYP2C9*2/*2 and CYP2C9*2/*3 was detected .Two kinds of allele G and A were detected for VKORC1(‐1639G/A) ,in which VKORC1‐1639G/G type was detected in 2 cases ,VKORC1‐1639G/A type was detected in 39 cases and VKORC1‐1639A/A type was detected in187 cases ,compared with the sequencing method ,the results of the fluorescence PCR‐melting curve method were completely consistent .Conclusion Xinjiang Hui population also has CYP2C9 gene *2 ,*3 loci and VKORC1 gene(‐1639G/A) locus polymorphism ,their occurrence frequency has a certain difference with Xingjiang Uygur and other regional populations ,the adopted fluorescence PCR‐melting curve method used in the gene polymorphism detection can meet clinical detection requirements .

Research progress in CYP2C9 and VKORC1 gene polymorphism and individualized warfarin therapeutic regimen / 解放军医学杂志

Warfarin is still the most clinically used oral anti-coagulant despite of its narrow therapeutic index and high risk of hemorrhage. The mean daily dose of warfarin varies widely from patient to patient, and to achieve the same therapeutic effect, the daily dose of warfarin could be varied over 20-fold. The variability in warfarin dosage depends on several factors, including gene polymorphisms, index of body mass, age and other drugs, and these factors compelled the clinicians to individualize warfarin dosage in order to optimize the therapeutic regimen. A number of genes are involved in metabolism of warfarin, such as cytochrome P450 2C9 (CYP2C9), vitamin K epoxide reductase complex subunit 1 (VKORC1), cytochrome P450 4F2 (CYP4F2), gamma-glutamylcarboxylase (GGCX), etc. Of them CYP2C9 and VKORC1 are the emphasis of current researches. The association between the polymorphism of CYP2C9 and VKORC1 and individualized warfarin therapeutic regimen are mainly discussed in this paper.

Influence of Vitamin K Epoxide Reductase Complex 1 Gene Polymorphisms on Anticoagulation with Acenocoumarol in Patients with Cerebral Venous Thrombosis.

Aims: Acenocoumarol, a commonly prescribed oral anticoagulant drug, exhibits wideinter-individual variability in response. This study aimed at evaluating the contribution of genetic variations in Vitamin K epoxide reductase complex, subunit 1 (VKORC1), to variability in the response to acenocoumarol, in patients with cerebral venous thrombosis (CVT). Place and Duration of Study: National Institute of Mental Health and Neuro Sciences, Bangalore, India, between September 2009 and January 2013. Methodology: 476 acenocoumarol-treated aseptic CVT patients (153 males, 323 females) were genotyped for VKORC1 -1639G>A and 1173C>T polymorphisms. Mean daily acenocoumarol dose for achieving and maintaining the optimum international normalized ratio (INR) was calculated for different genotypes. Results: Genotype distribution of VKORC1-1639G>A was as follows: 69.7% were wild,25.6% heterozygous and 4.6%, mutant. Mean acenocoumarol dose required to achieve the optimum INR was lower in heterozygous (1.82±0.71mg/day) and homozygous mutants (1.75±0.69mg/day) when compared to wild type patients (2.31±0.89mg/day). Bearing the VKORC1 -1639A allele independently increased the odds of requiring a low dose (Adjusted OR 3.9; 95% CI 1.97-7.73; p<0.0001). Significant differences in dose requirement during maintenance phase were observed in patients of different genotypes. VKORC1 -1639G>A and 1173C>T were observed to be tightly linked (r2=0.98) and no difference in the genotype distributions was observed between the two polymorphisms. Factors such as age and co-medication with phenytoin were also found to influence the drug dosage. Conclusion: Our findings support the use of VKORC1 genotyping during anticoagulation with acenocoumarol in patients with CVT.

Associations of POR polymorphisms and warfarin stable maintenance dose in Han Chinese patients / 中国药理学通报

Aim To explore the effect of genetic poly-morphisms of POR on the stable warfarin maintenance doses in Han Chinese patients receiving mechanical heart valve replacement. Methods The association between POR gene polymorphisms and warfarin doses of 185 Han Chinese patients were investigated through ANOVA or t test. SNPs of POR and VKORC1 were de-tected by Sequenom? DNA MassArray genotyping method. CYP2C9*3 was genotyped by polymerase chain reaction-restriction fragment length polymorphism method ( PCR-RFLP ) . Patients ’ clinical characteris-tics, INR value and daily dose were obtained from their medical records. Statistical analysis was performed by SPSS 21. 0 software. Results No mutant carriers of POR rs17148944 , POR rs56256515 and rs72553971 were found in this study. The genotype frequencies of other SNPs were in accordance with Hardy-Weinberg e-quilibrium. In the group of patients with CYP2C9*1*1 , the mutant type carriers ( T carriers ) of POR rs17685 had a significantly higher dose than CC carri-ers(3. 50 ± 1. 07) mg·d-1 vs (3. 14 ± 0. 94) mg· d-1,P =0. 03. Also, in the group of patients with CYP2 C9*1*1 and VKORC1 rs9934438 G allele carri-ers, the mutant type carriers ( T carriers ) of POR rs17685 had a significantly higher dose than CC carri-ers(4. 76 ± 0. 90) mg·d-1 vs (4. 08 ± 1. 03) mg· d-1 ,P=0. 04. No significant difference was found in different genotypes of POR rs2868177 . Conclusion These results illustrate that POR rs17685 T carrier is closely associated with a higher warfarin maintenance dose, suggesting that this SNP is useful for clinical guidance of warfarin.

Comparison on serum biomarkers for anovulatory and ovulatory dysfunctional uterine bleeding in Lizu females

OBJECTIVE@#To screen, identify, and compare the serum biomarkers between anovulatory dysfunctional uterine bleeding (ADUB) and ovulatory dysfunctional uterine bleeding (ODUB) in Lizu females.@*METHODS@#The subjects included 128 ADUB patients, 63 ODUB patients, and 93 controls. The serum and supernate of the subjects' mense were collected and stored at -80 °C until use. Differential proteins in the sera of three groups were screened using surface-enhanced laser desorption ionization time-of-flight mass spectrometry. The screened proteins were then identified by tricine-SDS-PAGE gel and spectrometry. Protein expression levels in the menses of ADUB, ODUB, and control subjects were determined using ELISA, RT-PCR, and Western blotting. SPSS 14.1 was used for statistical analysis and chart drawing (α = 0.05).@*RESULTS@#Three differential protein peaks with peak values of 11.80, 13.59, and 14.68 km/z were screened and identified as serum amyploid protein A (SAA), vascular endothelial growth factor, and vitamin K epoxide reductase, respectively. The SAA was highly expressed in the menses of ADUB and ODUB patients but poorly expressed in the controls. The vascular endothelial growth factor was highly expressed in the menses of ODUB and controls but poorly expressed in ADUB patients. Meanwhile, the vitamin K epoxide reductase was highly expressed in the menses of ADUB and control subjects but poorly expressed in ODUB patients.@*CONCLUSIONS@#The SAA is the common serum biomarker of ADUB and ODUB. ADUB may be related to angiogenesis impairment, whereas ODUB may be associated with blood coagulation disruption.

Inter and intra ethnic variation of vitamin K epoxide reductase complex and cytochrome P450 4F2 genetic polymorphisms and their prevalence in South Indian population.

BACKGROUND: Genetic variation in the vitamin K epoxide reductase complex (VKORC1) and cytochrome P450 4F2 (CYP4F2) genes were found to be strongly associated with the oral anticoagulant (OA) dose requirement. The distribution of genetic variation in these two genes was found to show large inter‑ and intra‑ethnic difference. MATERIALS AND METHODS: A total of 470 unrelated, healthy volunteers of South Indians of either sex (age: 18‑60 years) were enrolled for the study. A 5 ml of venous blood was collected and the genomic deoxyribonucleic acid (DNA) was extracted by using phenol‑chloroform extraction method. Real‑time quantitative polymerase chain reaction (RT‑PCR) method was used for genotyping. RESULTS: The variant allele frequencies of VKORC1 rs2359612 (T), rs8050894 (C), rs9934438 (T) and rs9923231 (A) were found to be 11.0%, 11.8%, 11.7% and 12.0%, respectively. The variant allele VKORC1 rs7294 was (80.1%) more frequent and the variant allele CYP4F2 * 3 was found to be 41.8% in South Indians. The allele, genotype and haplotype frequencies of VKORC1 and CYP4F2 gene were distinct from other compared HapMap populations (P < 0.0001). CONCLUSION: The findings of our study provide the basic genetic information for further pharmacogenetic based investigation of OA therapy in the population.

Relationship between VKORC1 single nucleotide polymorphism 1173C>T, bone mineral density & carotid intima-media thickness.

Background & objectives: The effects of vitamin K-dependent proteins in bone mineralization and vascular calcification and the implication of vitamin K epoxide reductase gene (VKORC1) 1173C>T polymorphism in warfarin sensitivity are well known. The main objective of the study was to investigate the relationship between VKORC1 1173C>T polymorphism, bone mineral density (BMD), and atherosclerosis (evaluated by intima-media thickness of the carotid artery and the presence of calcified plaques) in patients suspected to have osteoporosis or osteopenia and referred for BMD determination. Methods: VKORC1 1173C>T polymorphism was evaluated in 239 consecutive patients referred by their physicians for BMD measurement (dual energy X-ray absorptiometry at L2-L4 lumbar spine, femoral neck and total hip). Ultrasonography of the carotid arteries was performed, intima-media thickness (IMT) was measured and the presence of atherosclerotic calcified plaques was recorded. Results: In the patients with osteoporosis and osteopenia there was a higher frequency of TT genotype of VKORC1 1173C>T (P=0.04). The TT genotype was significantly more frequent in the osteoporotic group compared to the osteopenic group (P=0.01). The mean age and body mass index were lower in the patients with normal BMD and TT genotype (P=0.02, P=0.03). There was no correlation between the IMT and VKORC1 1173C>T genotype but the TT genotype had a significant association with the presence of calcified atherosclerotic plaques (P=0.05). This finding was not correlated with normal or pathologic BMD. Interpretation & conclusions: VKORC1 1173C>T polymorphism (TT genotype) was associated with osteoporosis and calcified plaques in the carotid artery in patients referred for BMD measurement. Different mechanisms are probably involved in these associations. TT genotype may serve as a potential genetic marker for the risk of OP and ATS.

Decreased Expression of Vitamin K Epoxide Reductase Complex Subunit 1 in Kidney of Patients with Calcium Oxalate Urolithiasis / 华中科技大学学报（医学）（英德文版）

Urinary prothrombin fragment 1 (UPTF1) is a potent inhibitor of urinary stone formation.UPTF1 exerts such inhibitory effect by effective γ-carboxylation in which vitamin K epoxide reductase complex subunit 1 (VKORC1),the rate-limiting enzyme,is involved.This study examined the correlation between VKORC1 expression and calcium oxalate urolithiasis.The renal cortex samples were obtained from patients undergoing nephrectomy and then divided into 3 groups:urolithiasis group,control group A [hydronephrosis-without-stone (HWS) group],control group B (normal control group).The localization and expression of VKORC 1 in renal tissues were determined by using immunohistochemistry,immunofluorescence microscopy,Western blotting and SYBR Green Ⅰreal-time reverse-transcription PCR.The rapid amplification of cDNA ends (RACE) were conducted to obtain the 3'- and 5'-untranslated region (UTR) of VKORC1.The results showed that VKORC1was located in the cytoplasm of renal tubular epithelial cells.The expression of VKORC 1 in the urolithiasis group was significantly lower than that in the other two control groups (P＜0.05).Moreover,the 3'- and 5'-UTR sequence of the VKORC 1 gene was successfully cloned.No insertion or deletion was found in the 3'- and 5'-UTR.However,a 171-bp new base sequence was discovered in the upstream of 5'-UTR end in the urolithiasis group.It was concluded that the decreased expression of VKORC1 may contribute to the development of calcium oxalate urolithiasis in the kidney.